Li Yingbo, Gao Runhong, Zong Yingjie, Guo Guimei, Zhang Wenqi, Chen Zhiwei, Guo Jiao, Liu Chenghong
Biotech Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China.
Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China.
Plants (Basel). 2025 Jul 23;14(15):2267. doi: 10.3390/plants14152267.
Abiotic stress can reprogram the gametophytic pathway; the mechanisms by which floral bud pre-treatment influences microspore embryogenesis initiation remain unclear. In this study, we use bisulfite sequencing, sRNA-seq, and RNA-seq to analyze the dynamic changes in rice microspores under different cold treatment durations. Our results showed that a 10-day cold treatment is essential for CXJ microspore embryogenesis initiation. DNA methylation levels showed a slight change at CG, CHG, and CHH sites under cold treatment. The number of both hyper- and hypomethylated DMRs increased over cold treatment, with more hypermethylated DMRs at 5 and 10 dpt. Hypermethylated DMRs were more frequently in the TSS region compared to hypomethylated DMRs. The proportion of 24 nt sRNAs increased upon cold stress, with more downregulated than upregulated sRNAs at 10 dpt. The number of DMR target DEGs increased from 5 to 10 dpt. Promoter hypomethylation at the CHH site was more frequently associated with DEGs. These outcomes suggested that the RdDM pathway participates in the initiation of rice ME. GO analysis indicated that DMR target DEGs at 10 dpt were enriched in responses to chemical stimuli, biological processes, and stress responses. An auxin-related gene, , was further identified. Its upregulation, potentially mediated by the RdDM pathway, may play a crucial role in the initiation of rice ME. This study provides more information on epigenetic mechanisms during rice ME.
非生物胁迫可重新编程配子体途径；花芽预处理影响小孢子胚胎发生起始的机制尚不清楚。在本研究中，我们使用亚硫酸氢盐测序、小RNA测序和RNA测序来分析不同冷处理持续时间下水稻小孢子的动态变化。我们的结果表明，10天的冷处理对于CXJ小孢子胚胎发生起始至关重要。冷处理下，CG、CHG和CHH位点的DNA甲基化水平有轻微变化。随着冷处理时间延长，高甲基化和低甲基化差异甲基化区域（DMR）的数量均增加，在处理后5天和10天高甲基化DMR更多。与低甲基化DMR相比，高甲基化DMR更频繁地出现在转录起始位点（TSS）区域。冷胁迫下24 nt小RNA的比例增加，在处理后10天下调的小RNA比上调的更多。DMR靶标差异表达基因（DEG）的数量从处理后5天到10天增加。CHH位点的启动子低甲基化更频繁地与DEG相关。这些结果表明RNA介导的DNA甲基化（RdDM）途径参与水稻小孢子胚胎发生的起始。基因本体（GO）分析表明，处理后10天的DMR靶标DEG在对化学刺激的反应、生物过程和应激反应中富集。进一步鉴定了一个生长素相关基因。其上调可能由RdDM途径介导，可能在水稻小孢子胚胎发生起始中起关键作用。本研究提供了关于水稻小孢子胚胎发生过程中表观遗传机制的更多信息。
